* samtools-0.1.3-21 (286)

[samtools.git] / bam.h

diff --git a/bam.h b/bam.h
index 4045684230a7cba886a0ed0fa390db3340866f91..eb4a375bdc236d9954ef69975f101ea07741fac4 100644 (file)
--- a/bam.h
+++ b/bam.h
@@ -315,6 +315,9 @@ extern "C" {
         */
        bam_header_t *sam_header_read2(const char *fn_list);
 
+       bam_header_t *sam_header_read(tamFile fp);
+       int sam_header_parse(bam_header_t *h);
+
 #define sam_write1(header, b) bam_view1(header, b)
 
        /*!
@@ -404,11 +407,12 @@ extern "C" {
        } while (0)
 
        /*!
-         @abstract       Print an alignment to the standard output in TAM format.
+         @abstract       Format a BAM record in the SAM format
          @param  header  pointer to the header structure
          @param  b       alignment to print
+         @return         a pointer to the SAM string
         */
-       void bam_view1(const bam_header_t *header, const bam1_t *b);
+       char *bam_format1(const bam_header_t *header, const bam1_t *b);
 
        /*!
          @abstract    Merge multiple sorted BAM.
@@ -511,17 +515,6 @@ extern "C" {
         */
        int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf);
 
-       /*!
-         @abstract         A more convenient interface to bam_plbuf_push()
-         @param  fp        BAM file handler
-         @param  func      user defined function
-         @param  func_data user provided data
-
-         @discussion The file position indicator must be placed right
-         before the start of an alignment. See also bam_plbuf_push().
-        */
-       int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data);
-
        struct __bam_lplbuf_t;
        typedef struct __bam_lplbuf_t bam_lplbuf_t;
 
@@ -599,6 +592,7 @@ extern "C" {
        void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end);
 
        void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data);
+       uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2]); // an alias of bam_aux_get()
        uint8_t *bam_aux_get(bam1_t *b, const char tag[2]);
        int32_t bam_aux2i(const uint8_t *s);
        float bam_aux2f(const uint8_t *s);